Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

Post-Doctoral position in brain imaging and computational morphometry – University of Geneva
by Narly Golestani 12 Feb '13

12 Feb '13

Post-Doctoral applications are invited in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland. Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise. Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills. We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience. The position is available immediately, and applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani(a)unige.ch.

1 1

entorhinal cortex volume question
by Cat Chong 29 Jan '13

29 Jan '13

Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine

3 4

22 Jan '13

Dear FS-experts, I'm trying to follow the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness to get volumetric stats etc on a functional ROI derived from marsbar. The tutorial looks all clear to me, however, I have already problems at the first step. If I want to view the ROI I see a big orange square instead of the specific region. This almost fills the whole brain. command: tkmedit -f avg152T1.nii -overlay DLPFC.nii -fthresh 0.5 I created the DLPFC.nii in MarsBar (v. 0.42): "ROI definition" > "Export" > "Export ROI to image" (select: DLPFC_roi.mat) > from image (select: avg152T1.nii) > save as DLPFC.nii If I view the ROI on marsbar it looks good. Did I miss some prior step, or is something else wrong? Thanks in advance! Best wishes, Cédric ------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Brain and Cognition Weesperplein 4; Room 3.07 1018 XA Amsterdam The Netherlands E P.C.M.P.Koolschijn(a)uva.nl W http://home.medewerker.uva.nl/p.c.m.p.koolschijn/ ------------------------------------------------------------

2 3

applying distortion correction output from epi_reg in fsl to freesurfer
by Ted Satterthwaite 04 Jan '13

04 Jan '13

Hi Bruce, Doug, and FreeSurfer Team, We have calculated coregistrations between bold timeseries and T1 images using BBR & distortion correction as implemented in the epi_reg utility in FSL5. We would like to map our functional timeseries to surface space for connectivity analyses (analagous to papers by Yeo & Buckner). Normally, without distortion correction, we would use tkregister tp convert the rigid body coregistration calculated in fsl by flirt(.mat) to a register.dat file, and then use mri_vol2surf to birng the data to surface space. However, with distortion correction, the coregistration between the epi & T1 is represented as a deformation field (_warp.nii.gz). Is there a way for FreeSurfer to read this warp and use the information? We could of course simply do a two-step registration by moving our epi data into T1 space first using FSL and then use FreeSurfer to get it to the surface, but that would involve an extra interpolation. Are the ways to do this in one step using our already-calculated & QA'd deformation fields from FSL? Thanks so much for your time & advice. Best, Ted Satterthwaite

2 4

motion correction
by O'Shea,Andrew 04 Jan '13

04 Jan '13

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew

2 1

fscalc / mris_calc problem
by Fred Lado 03 Jan '13

03 Jan '13

Hi FreeSurfer Gurus, I am having difficulty invoking the 'upl' and 'lrl' operations in mris_calc. The following is the message I get for 'upl': /usr/local/freesurfer/bin/fscalc rh.dat.mgh upl 20 --o tmp.mgh freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin Fred-Lados-MacBook-Pro.local 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64 mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh mri_convert rh.dat.mgh ./tmpdir.fscalc.5004/tmp.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from rh.dat.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, -1) writing to ./tmpdir.fscalc.5004/tmp.mgh... ---------------------- mris_calc -o ./tmpdir.fscalc.5004/tmp.mgh ./tmpdir.fscalc.5004/tmp.mgh upl 20 Unknown operation upl failed. No such file or directory Fred Lado, MD PhD Director, Neurology Service - Moses & North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: ladofred(a)gmail.com

3 4

white/gray surface and volumetric segmentation (aseg) difference...
by Gonzalo Rojas Costa 31 Dec '12

31 Dec '12

Hi: With some mprage images, I got differences in the volumetric segmentation (aseg) of the cortex and the white/gray surface... Why ?... I know that both methods are totally different... In the aseg I got some bad segmentation of the cortex, but it in the white/gray surface I got very better results... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

Re: [Freesurfer] clarifications about running bedpost instead of tracl-all step 2
by Anastasia Yendiki 31 Dec '12

31 Dec '12

Hi Prerona - The only way to fix this problem is to provide a gradient table that is correct. For that you have to go back to the person or program that was the source of your gradient tables. You can check if your inputs are correct by running a simple tensor fit and looking at the eigenvectors like I showed you. If your inputs are wrong, tractography won't work. If your inputs are correct and tractography doesn't work, I can try to help with that. Good luck and happy new year! a.y On Mon, 31 Dec 2012, s0675204 wrote: > Hi Anastasia > > thanks so much for looking at this. I can see how the directions are > wrong. Do you have any idea how I can fix this problem? > > best wishes, > > Prerona > > > On 28 December 2012 12:03, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> >> Hi Prerona - I'm attaching a screenshot of your eigenvectors (dmri/dtifit_V1.nii.gz) on your FA map (dmri/dtifit_FA.nii.gz). I've marked the corpus callosum, where the eigenvectors should be oriented left to right, and the cingulum, where the eigenvectors should be oriented anterior to posterior. There's something wrong with your inputs, most likely the bvecs/bvals aren't correct. >> >> Hope this helps, >> a.y >> >> >> On Thu, 27 Dec 2012, s0675204 wrote: >> >>> Hi Anastasia, >>> >>> Thank you so much for your quick and excellent help, as usual. >>> >>> I am sorry to bother you again, but I looked at your emails on the >>> archives about this and they say that I should look at the gradient >>> tables and the eigenectors (dmri/dtifit_V1.nii.gz) >>> I looked at these but I could not spot a problem. Do you think it >>> would be possible for you to have a look if I uploaded my files? >>> >>> best wishes, >>> >>> Prerona >>> >>> >>> On 22 December 2012 11:04, Anastasia Yendiki >>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> >>>> There are several threads about this in the archives. You need to look at >>>> the eigenectors in dmri/dtifit_V1.nii.gz and check that they are oriented in >>>> a way that makes sense with the anatomy. >>>> >>>> >>>> On Sat, 22 Dec 2012, s0675204 wrote: >>>> >>>>> Hi >>>>> >>>>> No I did not. Actually, I'm not sure how to do that. Is there any >>>>> information on that somewhere I could look up? >>>>> >>>>> best wishes, >>>>> >>>>> Prerona >>>>> >>>>> >>>>> On 21 December 2012 15:47, Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> >>>>>> This doesn't look right. Are you certain that your gradient table is >>>>>> correct? Have you looked at the eigenvectors of the tensor fit to make >>>>>> sure >>>>>> they're in the right orientation? >>>>>> >>>>>> >>>>>> On Fri, 21 Dec 2012, s0675204 wrote: >>>>>> >>>>>>> Thank you so much for your help! Sorry if I asked something that has >>>>>>> already asked on the mailing list >>>>>>> >>>>>>> I tried changing the threshold but that did not help. I am following >>>>>>> exactly the instructions here >>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs >>>>>>> >>>>>>> (Except I changed the file names >>>>>>> >>>>>>> So, the command I used was: >>>>>>> >>>>>>> freeview -v >>>>>>> /home/canlilab/SBU/data/tracula_test/00075/dmri/dtifit_FA.nii.gz \ >>>>>>> >>>>>>> >>>>>>> /home/canlilab/SBU/data/tracula_test/00075/dpath/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>> \ >>>>>>> >>>>>>> >>>>>>> /home/canlilab/SBU/data/tracula_test/00075/dpath/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>> &) >>>>>>> >>>>>>> Here is a screenshot attached. Should I also email you my files? >>>>>>> >>>>>>> best wishes, >>>>>>> >>>>>>> Prerona >>>>>>> >>>>>>> >>>>>>> On 20 December 2012 16:44, Anastasia Yendiki >>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Hi Prerona - As I've mentioned to others, you can ignore the >>>>>>>> "Degenerate >>>>>>>> spline segment" message. >>>>>>>> >>>>>>>> I can't tell what you mean by "only traced a part of the trac". Can you >>>>>>>> see >>>>>>>> the rest of it when you play with the threshold? Are you reconstructing >>>>>>>> only >>>>>>>> the ILF? If not, do the other pathways look ok? Can you send a >>>>>>>> screenshot >>>>>>>> of >>>>>>>> what you see when you run the "freeview -tv ..." command from the >>>>>>>> tutorial? >>>>>>>> >>>>>>>> Thanks, >>>>>>>> a.y >>>>>>>> >>>>>>>> >>>>>>>> On Mon, 17 Dec 2012, s0675204 wrote: >>>>>>>> >>>>>>>>> Hello >>>>>>>>> >>>>>>>>> I have been running trac-paths, and thought it finishes with a message >>>>>>>>> saying no errors, >>>>>>>>> I get an error saying ERROR: Degenerate spline segment in the >>>>>>>>> intermediate message logs >>>>>>>>> >>>>>>>>> Also I looked at the result using this command: >>>>>>>>> freeview -v >>>>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>>>> \ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>>>> & >>>>>>>>> >>>>>>>>> but it had only traced a part of the trac on one side and nothing on >>>>>>>>> the other side >>>>>>>>> >>>>>>>>> Can you help me understand what went wrong and how to fix it? >>>>>>>>> >>>>>>>>> Thank you so much for your help! >>>>>>>>> >>>>>>>>> best wishes, >>>>>>>>> >>>>>>>>> Prerona >>>>>>>>> >>>>>>>>> >>>>>>>>>>> On 12 December 2012 11:57, Anastasia Yendiki >>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 1) Can't hurt to delete. >>>>>>>>>>>> 2) Yes. >>>>>>>>>>>> 3) Yes. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Wed, 12 Dec 2012, s0675204 wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hello, >>>>>>>>>>>>> >>>>>>>>>>>>> thank you for your help with the first steps of running Tracula. >>>>>>>>>>>>> >>>>>>>>>>>>> I was trying to run trac-all step 3 (paths), but was getting an >>>>>>>>>>>>> error >>>>>>>>>>>>> with the mergedph1samples file. I saw on the mailbase that you >>>>>>>>>>>>> have >>>>>>>>>>>>> suggested to run bedpost directly to fix this >>>>>>>>>>>>> >>>>>>>>>>>>> I have 3 questions about this: >>>>>>>>>>>>> >>>>>>>>>>>>> 1) do I need to delete any of the (temporary?) files or folders >>>>>>>>>>>>> created by trac-all step 2 before running bedpost >>>>>>>>>>>>> >>>>>>>>>>>>> 2) should I run bedpost INSTEAD of trac-all step 2 for the >>>>>>>>>>>>> remaining >>>>>>>>>>>>> subjects? >>>>>>>>>>>>> >>>>>>>>>>>>> 3) you have suggested on the list to run bedpost as: >>>>>>>>>>>>> bedpostx /usr/local/freesurfer/subjects/C001/dmri >>>>>>>>>>>>> is this the same dmri folder as created by tracula step 1 (for >>>>>>>>>>>>> each >>>>>>>>>>>>> subject) >>>>>>>>>>>>> >>>>>>>>>>>>> Thank you so much for your help with this - I really appreciate it >>>>>>>>>>>>> >>>>>>>>>>>>> best wishes >>>>>>>>>>>>> >>>>>>>>>>>>> Prerona >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 10 December 2012 19:54, Anastasia Yendiki >>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> I'm guessing that this shows up in the scripts/trac-all.log of a >>>>>>>>>>>>>> particular >>>>>>>>>>>>>> subject? Then it applies to that subject. >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, 10 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hello >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> My trac- preproc has completed. However, I am confused about the >>>>>>>>>>>>>>> status message. It says: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>>> trac-preproc finished without error at Mon Dec 10 16:32:20 EST >>>>>>>>>>>>>>> 2012 >>>>>>>>>>>>>>> ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Does this mean it was completed succesfully for everyone or >>>>>>>>>>>>>>> everyone >>>>>>>>>>>>>>> but that 00387 person? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Is there any way I can verify this? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> thank you so much for your help >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 8 December 2012 13:38, Anastasia Yendiki >>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> In your dmrirc, you define multiple subjects, but only one >>>>>>>>>>>>>>>> bvecfile >>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>> bvalfile that are used for all subjects. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Sat, 8 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> the values are the same but each subject has an individual >>>>>>>>>>>>>>>>> bvec >>>>>>>>>>>>>>>>> & >>>>>>>>>>>>>>>>> bval >>>>>>>>>>>>>>>>> file. so it depends on how the script will read it? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On 8 December 2012 00:03, Anastasia Yendiki >>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Are the bvecs/bvals not the same for all subjects? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> oh! i thought this was how these were meant to be! i will do >>>>>>>>>>>>>>>>>>> that. >>>>>>>>>>>>>>>>>>> sadly i left the lab and came home for the day but i will >>>>>>>>>>>>>>>>>>> try >>>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>>> as >>>>>>>>>>>>>>>>>>> soon as i am back and let you know! >>>>>>>>>>>>>>>>>>> thank you so much! do we have to do this for each subject or >>>>>>>>>>>>>>>>>>> just >>>>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>>>> time? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On 7 December 2012 23:51, Anastasia Yendiki >>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> I see. Can you try formatting them in columns (1 column for >>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>> bvals >>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>> 3 >>>>>>>>>>>>>>>>>>>> columns for the bvecs)? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> yes! these are the original files >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> well these are the files i pointed to in my config file. >>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>> i >>>>>>>>>>>>>>>>>>>>> think >>>>>>>>>>>>>>>>>>>>> the script copies them over to the dmrirc folder? >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On 7 December 2012 23:38, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Yes, I can see that each of the bvecs/bvals files is one >>>>>>>>>>>>>>>>>>>>>> long >>>>>>>>>>>>>>>>>>>>>> line. >>>>>>>>>>>>>>>>>>>>>> Was >>>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>>> the case for the original files that you specified in the >>>>>>>>>>>>>>>>>>>>>> dmrirc? >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hi Anastasia >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I had attached the files, but maybe they did not go >>>>>>>>>>>>>>>>>>>>>>> through >>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>> mailing list? So I am sending them to your email id. >>>>>>>>>>>>>>>>>>>>>>> Hope >>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>> okay >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>>>>>>>>>>>>>>> From: s0675204 <s0675204(a)sms.ed.ac.uk> >>>>>>>>>>>>>>>>>>>>>>> Date: 7 December 2012 19:44 >>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Freesurfer] Running Tracula: trac-preproc >>>>>>>>>>>>>>>>>>>>>>> exited >>>>>>>>>>>>>>>>>>>>>>> with >>>>>>>>>>>>>>>>>>>>>>> ERRORS >>>>>>>>>>>>>>>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Hello >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I think I spoke to soon! >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> It ended with errors again. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I get the error message: "bvecs and bvals don't have the >>>>>>>>>>>>>>>>>>>>>>> same >>>>>>>>>>>>>>>>>>>>>>> number >>>>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>>>> entries" >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I saw on some older messages on the mail-base you said >>>>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>>>> we >>>>>>>>>>>>>>>>>>>>>>> need >>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>> check that the number of entries in the bvals is same as >>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>> bvecs >>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>> 3 times as much as the number of volumes. I have checked >>>>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>> the case >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I am wondering if it is some formatting problem? there >>>>>>>>>>>>>>>>>>>>>>> are >>>>>>>>>>>>>>>>>>>>>>> no >>>>>>>>>>>>>>>>>>>>>>> spaces >>>>>>>>>>>>>>>>>>>>>>> at the end of the file. and there are no end of line >>>>>>>>>>>>>>>>>>>>>>> markers >>>>>>>>>>>>>>>>>>>>>>> either. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Please could you advise me? I have attached the files >>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>> also >>>>>>>>>>>>>>>>>>>>>>> pasted >>>>>>>>>>>>>>>>>>>>>>> the contents below >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> My config file is still the same (as pasted below) >>>>>>>>>>>>>>>>>>>>>>> except >>>>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>>>> tried >>>>>>>>>>>>>>>>>>>>>>> changing >>>>>>>>>>>>>>>>>>>>>>> nb0 to 2 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> (# Number of low-b images >>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>> set nb0 = 2) >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> ========================================================= >>>>>>>>>>>>>>>>>>>>>>> bvals: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 0 800 800 800 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 800 800 0 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>>>> 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> bvecs: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> 0 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>>>>>>>>>>>>>>> 0.85177010297775 >>>>>>>>>>>>>>>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 >>>>>>>>>>>>>>>>>>>>>>> 0.7912425994873 >>>>>>>>>>>>>>>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>>>>>>>>>>>>>>> 0.44143822789192 >>>>>>>>>>>>>>>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 >>>>>>>>>>>>>>>>>>>>>>> 0.43744987249374 >>>>>>>>>>>>>>>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>>>>>>>>>>>>>>> 0.00979638285934 >>>>>>>>>>>>>>>>>>>>>>> 0 >>>>>>>>>>>>>>>>>>>>>>> 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>>>>>>>>>>>>>>> 0.85177010297775 >>>>>>>>>>>>>>>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 >>>>>>>>>>>>>>>>>>>>>>> 0.7912425994873 >>>>>>>>>>>>>>>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>>>>>>>>>>>>>>> 0.44143822789192 >>>>>>>>>>>>>>>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 >>>>>>>>>>>>>>>>>>>>>>> 0.43744987249374 >>>>>>>>>>>>>>>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>>>>>>>>>>>>>>> 0.00979638285934 >>>>>>>>>>>>>>>>>>>>>>> 0 >>>>>>>>>>>>>>>>>>>>>>> -0.00687454920262 0.96709138154983 0.62002921104431 >>>>>>>>>>>>>>>>>>>>>>> 0.52092331647872 >>>>>>>>>>>>>>>>>>>>>>> 0.18501849472522 -0.42448142170906 -0.44344407320022 >>>>>>>>>>>>>>>>>>>>>>> 0.15539556741714 >>>>>>>>>>>>>>>>>>>>>>> 0.60610836744308 0.88347893953323 0.71210372447967 >>>>>>>>>>>>>>>>>>>>>>> 0.30400663614273 >>>>>>>>>>>>>>>>>>>>>>> -0.23736105859279 -0.70398008823394 -0.85636389255523 >>>>>>>>>>>>>>>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>>>>>>>>>>>>>>> 0.51328992843627 >>>>>>>>>>>>>>>>>>>>>>> 0.93218487501144 0 -0.00687454920262 0.96709138154983 >>>>>>>>>>>>>>>>>>>>>>> 0.62002921104431 >>>>>>>>>>>>>>>>>>>>>>> 0.52092331647872 0.18501849472522 -0.42448142170906 >>>>>>>>>>>>>>>>>>>>>>> -0.44344407320022 >>>>>>>>>>>>>>>>>>>>>>> 0.15539556741714 0.60610836744308 0.88347893953323 >>>>>>>>>>>>>>>>>>>>>>> 0.71210372447967 >>>>>>>>>>>>>>>>>>>>>>> 0.30400663614273 -0.23736105859279 -0.70398008823394 >>>>>>>>>>>>>>>>>>>>>>> -0.85636389255523 >>>>>>>>>>>>>>>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>>>>>>>>>>>>>>> 0.51328992843627 >>>>>>>>>>>>>>>>>>>>>>> 0.93218487501144 0 0.05151799321174 -0.2540076971054 >>>>>>>>>>>>>>>>>>>>>>> -0.78447526693344 >>>>>>>>>>>>>>>>>>>>>>> 0.05591572076082 -0.46734625101089 -0.3037790954113 >>>>>>>>>>>>>>>>>>>>>>> 0.31549325585365 >>>>>>>>>>>>>>>>>>>>>>> 0.5914282798767 0.60493636131286 0.08063688874244 >>>>>>>>>>>>>>>>>>>>>>> -0.44614082574844 >>>>>>>>>>>>>>>>>>>>>>> -0.84422290325164 -0.81589156389236 -0.56895911693573 >>>>>>>>>>>>>>>>>>>>>>> -0.02196817658841 0.51983833312988 0.83259600400924 >>>>>>>>>>>>>>>>>>>>>>> 0.99861049652099 >>>>>>>>>>>>>>>>>>>>>>> 0.85606354475021 0.36184993386268 0 0.05151799321174 >>>>>>>>>>>>>>>>>>>>>>> -0.2540076971054 >>>>>>>>>>>>>>>>>>>>>>> -0.78447526693344 0.05591572076082 -0.46734625101089 >>>>>>>>>>>>>>>>>>>>>>> -0.3037790954113 >>>>>>>>>>>>>>>>>>>>>>> 0.31549325585365 0.5914282798767 0.60493636131286 >>>>>>>>>>>>>>>>>>>>>>> 0.08063688874244 >>>>>>>>>>>>>>>>>>>>>>> -0.44614082574844 -0.84422290325164 -0.81589156389236 >>>>>>>>>>>>>>>>>>>>>>> -0.56895911693573 -0.02196817658841 0.51983833312988 >>>>>>>>>>>>>>>>>>>>>>> 0.83259600400924 >>>>>>>>>>>>>>>>>>>>>>> 0.99861049652099 0.85606354475021 0.36184993386268 >>>>>>>>>>>>>>>>>>>>>>> On 7 December 2012 14:08, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Great, I love easy problems :) >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you! It's chugging away now >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On 7 December 2012 13:46, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hi Prerona - You need to uncomment the bvecfile and >>>>>>>>>>>>>>>>>>>>>>>>>> bvalfile >>>>>>>>>>>>>>>>>>>>>>>>>> definitions >>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>> your configuration file. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Hello >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I am trying to run Tracula on a set of dicoms files. >>>>>>>>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>>>>>>>> have >>>>>>>>>>>>>>>>>>>>>>>>>>> run >>>>>>>>>>>>>>>>>>>>>>>>>>> recon-all previously. >>>>>>>>>>>>>>>>>>>>>>>>>>> I am getting a message trac-preproc exited with >>>>>>>>>>>>>>>>>>>>>>>>>>> ERRORS >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Please can anyone advise me on this? >>>>>>>>>>>>>>>>>>>>>>>>>>> I have listed all the details (command, >>>>>>>>>>>>>>>>>>>>>>>>>>> error/output, >>>>>>>>>>>>>>>>>>>>>>>>>>> config >>>>>>>>>>>>>>>>>>>>>>>>>>> file) >>>>>>>>>>>>>>>>>>>>>>>>>>> below >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you so much for your help >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> DETAILS >>>>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>>>> command used: trac-all -prep -c >>>>>>>>>>>>>>>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>>>> error message >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>>>> canlilab@112-205:~/SBU/data/tracula$ trac-all -prep >>>>>>>>>>>>>>>>>>>>>>>>>>> -c >>>>>>>>>>>>>>>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: SUBJECTS_DIR is >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/recon_output >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: Diffusion root is >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula >>>>>>>>>>>>>>>>>>>>>>>>>>> Actual FREESURFER_HOME /home/canlilab/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>>>> trac-preproc -c >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/dmrirc.local >>>>>>>>>>>>>>>>>>>>>>>>>>> -log >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.log >>>>>>>>>>>>>>>>>>>>>>>>>>> -cmd >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.cmd >>>>>>>>>>>>>>>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/freesurfer/bin/trac-preproc >>>>>>>>>>>>>>>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>>>>>>>>>>>>>>> #@# Image corrections Fri Dec 7 10:42:30 EST 2012 >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 >>>>>>>>>>>>>>>>>>>>>>>>>>> greve >>>>>>>>>>>>>>>>>>>>>>>>>>> Exp >>>>>>>>>>>>>>>>>>>>>>>>>>> $ >>>>>>>>>>>>>>>>>>>>>>>>>>> reading from >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm... >>>>>>>>>>>>>>>>>>>>>>>>>>> Getting Series No >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: Found 44 files in >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075 >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: Scanning for Series Number 7 >>>>>>>>>>>>>>>>>>>>>>>>>>> Scanning Directory >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: found 42 files in series >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: loading series header info. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> RunNo = 6 >>>>>>>>>>>>>>>>>>>>>>>>>>> WARNING: Run 1 appears to be truncated >>>>>>>>>>>>>>>>>>>>>>>>>>> Files Found: 42, Files Expected (lRep+1): 2 >>>>>>>>>>>>>>>>>>>>>>>>>>> FileName >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> Identification >>>>>>>>>>>>>>>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>>>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>>>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>>>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>>>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>>>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>>>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>>>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>>>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>>>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>>>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>>>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>>>> Image information >>>>>>>>>>>>>>>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>>>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>>>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>>>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>>>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>>>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> ImgPos 772.3238 773.0634 185.5347 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolCenter 0.0000 0.0000 0.0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: sorting. >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: (128 128 40), nframes = 42, ismosaic=1 >>>>>>>>>>>>>>>>>>>>>>>>>>> Could not parse NUMARIS version string syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>>>> found in dicom tag 18,1020 (len = 3 != 6) >>>>>>>>>>>>>>>>>>>>>>>>>>> Repetition Time = 5500, TR = 5500 ms >>>>>>>>>>>>>>>>>>>>>>>>>>> PE Dir COL COL >>>>>>>>>>>>>>>>>>>>>>>>>>> AutoAlign matrix detected >>>>>>>>>>>>>>>>>>>>>>>>>>> AutoAlign Matrix --------------------- >>>>>>>>>>>>>>>>>>>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> FileName >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> Identification >>>>>>>>>>>>>>>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>>>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>>>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>>>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>>>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>>>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>>>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>>>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>>>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>>>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>>>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>>>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>>>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>>>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>>>> Image information >>>>>>>>>>>>>>>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>>>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>>>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>>>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>>>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>>>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> ImgPos 113.4156 146.2544 -24.5854 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>>>>>>>>>>>>>>> VolCenter 0.1478 26.0388 -1.8116 >>>>>>>>>>>>>>>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>>>>>>>>>>>>>>> sagrev = 0, correv =0, trarev = 0 >>>>>>>>>>>>>>>>>>>>>>>>>>> Vs = -0.0574949 -0.262456 0.963229 >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: no Siemens slice order reversal detected >>>>>>>>>>>>>>>>>>>>>>>>>>> (good!). >>>>>>>>>>>>>>>>>>>>>>>>>>> TR=5500.00, TE=93.00, TI=-1.00, flip angle=90.00 >>>>>>>>>>>>>>>>>>>>>>>>>>> i_ras = (-0.998346, 0.0151149, -0.0554726) >>>>>>>>>>>>>>>>>>>>>>>>>>> j_ras = (-3.31902e-08, -0.964826, -0.262891) >>>>>>>>>>>>>>>>>>>>>>>>>>> k_ras = (-0.0574949, -0.262456, 0.963229) >>>>>>>>>>>>>>>>>>>>>>>>>>> writing to >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz... >>>>>>>>>>>>>>>>>>>>>>>>>>> mri_probedicom --i >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dcminfo.dat >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> flip4fsl >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: input image orientation is LPS >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: input image determinant is 8.86231 >>>>>>>>>>>>>>>>>>>>>>>>>>> fslswapdim >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> x -y z >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> INFO: left-right orientation was flipped by >>>>>>>>>>>>>>>>>>>>>>>>>>> fslswapdim >>>>>>>>>>>>>>>>>>>>>>>>>>> fslorient -forceradiological >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> mv -f >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/bvecs >>>>>>>>>>>>>>>>>>>>>>>>>>> mv: cannot stat >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> `/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs': >>>>>>>>>>>>>>>>>>>>>>>>>>> No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>>>> Linux 112-205.psy.sunysb.edu >>>>>>>>>>>>>>>>>>>>>>>>>>> 2.6.32-279.5.2.el6.x86_64 >>>>>>>>>>>>>>>>>>>>>>>>>>> #1 >>>>>>>>>>>>>>>>>>>>>>>>>>> SMP >>>>>>>>>>>>>>>>>>>>>>>>>>> Fri >>>>>>>>>>>>>>>>>>>>>>>>>>> Aug >>>>>>>>>>>>>>>>>>>>>>>>>>> 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> trac-preproc exited with ERRORS at Fri Dec 7 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10:42:51 >>>>>>>>>>>>>>>>>>>>>>>>>>> EST >>>>>>>>>>>>>>>>>>>>>>>>>>> 2012 >>>>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> config file: >>>>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # dmrirc.example >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # This file contains commands that will be run by >>>>>>>>>>>>>>>>>>>>>>>>>>> trac-all >>>>>>>>>>>>>>>>>>>>>>>>>>> before >>>>>>>>>>>>>>>>>>>>>>>>>>> an >>>>>>>>>>>>>>>>>>>>>>>>>>> analysis. >>>>>>>>>>>>>>>>>>>>>>>>>>> # It is used to set all parameters needed for the >>>>>>>>>>>>>>>>>>>>>>>>>>> analysis. >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Remove a parameter from your dmrirc file if you >>>>>>>>>>>>>>>>>>>>>>>>>>> want >>>>>>>>>>>>>>>>>>>>>>>>>>> use >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> default >>>>>>>>>>>>>>>>>>>>>>>>>>> value. >>>>>>>>>>>>>>>>>>>>>>>>>>> # Parameters that don't have default values must be >>>>>>>>>>>>>>>>>>>>>>>>>>> specified. >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Any other commands that you might want to run >>>>>>>>>>>>>>>>>>>>>>>>>>> before >>>>>>>>>>>>>>>>>>>>>>>>>>> an >>>>>>>>>>>>>>>>>>>>>>>>>>> analysis >>>>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>>>> added >>>>>>>>>>>>>>>>>>>>>>>>>>> # to this file. >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Original Author: Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>>>>>> # CVS Revision Info: >>>>>>>>>>>>>>>>>>>>>>>>>>> # $Author: ayendiki $ >>>>>>>>>>>>>>>>>>>>>>>>>>> # $Date: 2011/05/24 06:47:12 $ >>>>>>>>>>>>>>>>>>>>>>>>>>> # $Revision: 1.3.2.3 $ >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Copyright © 2011 The General Hospital Corporation >>>>>>>>>>>>>>>>>>>>>>>>>>> (Boston >>>>>>>>>>>>>>>>>>>>>>>>>>> MA) >>>>>>>>>>>>>>>>>>>>>>>>>>> "MGH" >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Terms and conditions for use reproduction >>>>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>> contribution >>>>>>>>>>>>>>>>>>>>>>>>>>> # are found in the 'FreeSurfer Software License >>>>>>>>>>>>>>>>>>>>>>>>>>> Agreement' >>>>>>>>>>>>>>>>>>>>>>>>>>> contained >>>>>>>>>>>>>>>>>>>>>>>>>>> # in the file 'LICENSE' found in the FreeSurfer >>>>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>> here: >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # Reporting: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # FreeSurfer SUBJECTS_DIR >>>>>>>>>>>>>>>>>>>>>>>>>>> # T1 images and FreeSurfer segmentations are >>>>>>>>>>>>>>>>>>>>>>>>>>> expected >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>>>> found >>>>>>>>>>>>>>>>>>>>>>>>>>> here >>>>>>>>>>>>>>>>>>>>>>>>>>> # setenv SUBJECTS_DIR /path/to/recons/of/ducks >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Output directory where trac-all results will be >>>>>>>>>>>>>>>>>>>>>>>>>>> saved >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: Same as SUBJECTS_DIR >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set dtroot = $pre_data/tracula >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Subject IDs >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set subjlist = (00075 00104 00122 00200 00308 00369 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00387 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00400 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00422 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00452 00518 00568 00587 00624 00636 00686 00698 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00727 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00909 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00926 >>>>>>>>>>>>>>>>>>>>>>>>>>> 00933 00943 00983 00992 01049 01121 01329 01450 >>>>>>>>>>>>>>>>>>>>>>>>>>> 01509 >>>>>>>>>>>>>>>>>>>>>>>>>>> 01531 >>>>>>>>>>>>>>>>>>>>>>>>>>> 01678 >>>>>>>>>>>>>>>>>>>>>>>>>>> 01735 01746 01809 01843 01917 10039 10056 10089 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10165 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10171 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10227 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10238 10263 10314 10320 10326 10349 10407 10431 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10435 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10458 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10477 >>>>>>>>>>>>>>>>>>>>>>>>>>> 10499 10500 10636 10750 11209 12210 12357 12472 >>>>>>>>>>>>>>>>>>>>>>>>>>> 12645 >>>>>>>>>>>>>>>>>>>>>>>>>>> 13493 >>>>>>>>>>>>>>>>>>>>>>>>>>> 13958 >>>>>>>>>>>>>>>>>>>>>>>>>>> 14302 14481 14530 15329 15345 15864 16654 17267 >>>>>>>>>>>>>>>>>>>>>>>>>>> 17478 >>>>>>>>>>>>>>>>>>>>>>>>>>> 18337 >>>>>>>>>>>>>>>>>>>>>>>>>>> 18422 >>>>>>>>>>>>>>>>>>>>>>>>>>> 18530 19259 19377 19725 20071 20383 21413 23846 >>>>>>>>>>>>>>>>>>>>>>>>>>> 24115 >>>>>>>>>>>>>>>>>>>>>>>>>>> 24531 >>>>>>>>>>>>>>>>>>>>>>>>>>> 24781 >>>>>>>>>>>>>>>>>>>>>>>>>>> 25962 26314 26475 28822 30510 30571 30927 31034 >>>>>>>>>>>>>>>>>>>>>>>>>>> 31049 >>>>>>>>>>>>>>>>>>>>>>>>>>> 31237 >>>>>>>>>>>>>>>>>>>>>>>>>>> 31437 >>>>>>>>>>>>>>>>>>>>>>>>>>> 31471 31531 32131 32162 32222) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # In case you want to analyze only Huey and Louie >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: Run analysis on all subjects >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set runlist = (1 2 3 4 5 >>>>>>>>>>>>>>>>>>>>>>>>>>> 6 >>>>>>>>>>>>>>>>>>>>>>>>>>> 7 >>>>>>>>>>>>>>>>>>>>>>>>>>> 8 9 10 11 12 13 14 >>>>>>>>>>>>>>>>>>>>>>>>>>> 15 >>>>>>>>>>>>>>>>>>>>>>>>>>> 16 >>>>>>>>>>>>>>>>>>>>>>>>>>> 17 18 19 20 21 22 23 >>>>>>>>>>>>>>>>>>>>>>>>>>> 24 >>>>>>>>>>>>>>>>>>>>>>>>>>> 25 >>>>>>>>>>>>>>>>>>>>>>>>>>> 26 27 28 29 30 31 32 >>>>>>>>>>>>>>>>>>>>>>>>>>> 33 >>>>>>>>>>>>>>>>>>>>>>>>>>> 34 >>>>>>>>>>>>>>>>>>>>>>>>>>> 35 36 37 38 39 40 41 >>>>>>>>>>>>>>>>>>>>>>>>>>> 42 >>>>>>>>>>>>>>>>>>>>>>>>>>> 43 >>>>>>>>>>>>>>>>>>>>>>>>>>> 44 45 46 47 48 49 >>>>>>>>>>>>>>>>>>>>>>>>>>> 50 >>>>>>>>>>>>>>>>>>>>>>>>>>> 51 >>>>>>>>>>>>>>>>>>>>>>>>>>> 52 >>>>>>>>>>>>>>>>>>>>>>>>>>> 53 54 55 56 57 58 >>>>>>>>>>>>>>>>>>>>>>>>>>> 59 >>>>>>>>>>>>>>>>>>>>>>>>>>> 60 >>>>>>>>>>>>>>>>>>>>>>>>>>> 61 62 63 64 65 66 67 >>>>>>>>>>>>>>>>>>>>>>>>>>> 68 >>>>>>>>>>>>>>>>>>>>>>>>>>> 69 >>>>>>>>>>>>>>>>>>>>>>>>>>> 70 71 72 73 74 75 76 >>>>>>>>>>>>>>>>>>>>>>>>>>> 77 >>>>>>>>>>>>>>>>>>>>>>>>>>> 78 >>>>>>>>>>>>>>>>>>>>>>>>>>> 79 80 81 82 83 84 85 >>>>>>>>>>>>>>>>>>>>>>>>>>> 86 >>>>>>>>>>>>>>>>>>>>>>>>>>> 87 >>>>>>>>>>>>>>>>>>>>>>>>>>> 88 89 90 91 92 93 94 >>>>>>>>>>>>>>>>>>>>>>>>>>> 95 >>>>>>>>>>>>>>>>>>>>>>>>>>> 96 >>>>>>>>>>>>>>>>>>>>>>>>>>> 97 98 99 100 101 102) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Input diffusion DICOMs (file names relative to >>>>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>>>> # If original DICOMs don't exist these can be in >>>>>>>>>>>>>>>>>>>>>>>>>>> other >>>>>>>>>>>>>>>>>>>>>>>>>>> image >>>>>>>>>>>>>>>>>>>>>>>>>>> format >>>>>>>>>>>>>>>>>>>>>>>>>>> # but then bvecfile bvalfile and nb0 must be >>>>>>>>>>>>>>>>>>>>>>>>>>> specified >>>>>>>>>>>>>>>>>>>>>>>>>>> (see >>>>>>>>>>>>>>>>>>>>>>>>>>> below) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> set dcmroot = $pre_data/dti_dicoms >>>>>>>>>>>>>>>>>>>>>>>>>>> set dcmlist = (00075/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00104/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00122/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00200/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00308/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00369/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00387/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00400/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00422/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00452/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00518/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00568/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00587/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00624/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00636/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00686/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00698/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00727/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00909/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00926/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00933/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00943/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00983/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 00992/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01049/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01121/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01329/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01450/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01509/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01678/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01735/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01746/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01809/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01843/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 01917/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10039/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10056/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10089/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10165/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10171/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10227/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10238/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10263/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10314/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10320/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10326/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10349/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10407/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10431/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10435/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10458/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10477/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10499/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10500/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10636/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 10750/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 11209/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 12210/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 12357/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 12472/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 12645/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 13493/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 13958/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 14302/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 14481/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 14530/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 15329/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 15345/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 15864/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 16654/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 17267/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 17478/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 18337/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 18422/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 18530/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 19259/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 19377/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 19725/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 20071/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 20383/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 21413/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 23846/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 24115/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 24531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 24781/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 25962/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 26314/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 26475/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 28822/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 30510/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 30571/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 30927/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31034/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31049/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31237/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31437/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31471/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 31531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 32131/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 32162/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>>>> 32222/data_1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Diffusion gradient table >>>>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not MGH DICOMs >>>>>>>>>>>>>>>>>>>>>>>>>>> # Three-column format one row for each volume in the >>>>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>>>> set >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> #set bvecfile = >>>>>>>>>>>>>>>>>>>>>>>>>>> $pre_data/DTI_Analysis/00075/bvecs.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Diffusion b-value table >>>>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not MGH DICOMs >>>>>>>>>>>>>>>>>>>>>>>>>>> # Single-column format one value for each volume in >>>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>>>> set >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> #set bvalfile = >>>>>>>>>>>>>>>>>>>>>>>>>>> $pre_data/DTI_Analysis/00075/bvals.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Number of low-b images >>>>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set nb0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Perform registration-based B0-inhomogeneity >>>>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set dob0 = 0 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Input B0 field map magnitude DICOMs (file names >>>>>>>>>>>>>>>>>>>>>>>>>>> relative >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> #set b0mlist = (huey/fmag/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> dewey/fmag/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> louie/fmag/XXX-1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Input B0 field map phase DICOMs (file names >>>>>>>>>>>>>>>>>>>>>>>>>>> relative >>>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> #set b0plist = (huey/fphas/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> dewey/fphas/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>>> louie/fphas/XXX-1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Echo spacing for field mapping sequence (from >>>>>>>>>>>>>>>>>>>>>>>>>>> sequence >>>>>>>>>>>>>>>>>>>>>>>>>>> printout) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> #set echospacing = 0.7 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Perform registration-based eddy-current >>>>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set doeddy = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Rotate diffusion gradient vectors to match >>>>>>>>>>>>>>>>>>>>>>>>>>> eddy-current >>>>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Only used if doeddy = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set dorotbvecs = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Fractional intensity threshold for BET mask >>>>>>>>>>>>>>>>>>>>>>>>>>> extraction >>>>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>>>> low-b >>>>>>>>>>>>>>>>>>>>>>>>>>> images >>>>>>>>>>>>>>>>>>>>>>>>>>> # This mask is used only if usemaskanat = 0 >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0.3 >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set thrbet = 0.5 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by flirt? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set doregflt = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by >>>>>>>>>>>>>>>>>>>>>>>>>>> bbregister? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set doregbbr = 0 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # MNI template (the only option for inter-subject >>>>>>>>>>>>>>>>>>>>>>>>>>> registration >>>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>>>> version) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: >>>>>>>>>>>>>>>>>>>>>>>>>>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set mnitemp = >>>>>>>>>>>>>>>>>>>>>>>>>>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Use brain mask extracted from T1 image instead of >>>>>>>>>>>>>>>>>>>>>>>>>>> low-b >>>>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>>>> image? >>>>>>>>>>>>>>>>>>>>>>>>>>> # Has no effect if there is no T1 data >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set usemaskanat = 1 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Paths to reconstruct >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: All paths in the atlas >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set pathlist = ( lh.cst_AS rh.cst_AS \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.unc_AS rh.unc_AS \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.ilf_AS rh.ilf_AS \ >>>>>>>>>>>>>>>>>>>>>>>>>>> fmajor_PP fminor_PP \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.atr_PP rh.atr_PP \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.ccg_PP rh.ccg_PP \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.cab_PP rh.cab_PP \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.slfp_PP rh.slfp_PP \ >>>>>>>>>>>>>>>>>>>>>>>>>>> lh.slft_PP rh.slft_PP ) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Number of path control points >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5 >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set ncpts = 5 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # List of training subjects >>>>>>>>>>>>>>>>>>>>>>>>>>> # This text file lists the locations of training >>>>>>>>>>>>>>>>>>>>>>>>>>> subject >>>>>>>>>>>>>>>>>>>>>>>>>>> directories >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: $FREESURFER_HOME/trctrain/trainlist.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set trainfile = >>>>>>>>>>>>>>>>>>>>>>>>>>> $FREESURFER_HOME/trctrain/trainlist.txt >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Use long (more descriptive) directory hierarchy >>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>> saving >>>>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>>>> distributions? >>>>>>>>>>>>>>>>>>>>>>>>>>> # By default paths distributions are saved directly >>>>>>>>>>>>>>>>>>>>>>>>>>> under >>>>>>>>>>>>>>>>>>>>>>>>>>> $subjectname/dpath >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set dopathsubdirs = 0 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Number of MCMC burn-in iterations >>>>>>>>>>>>>>>>>>>>>>>>>>> # (Path samples drawn initially by MCMC algorithm >>>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>>> discarded) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 200 >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set nburnin = 200 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Number of MCMC iterations >>>>>>>>>>>>>>>>>>>>>>>>>>> # (Path samples drawn by MCMC algorithm and used to >>>>>>>>>>>>>>>>>>>>>>>>>>> estimate >>>>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>>>> distribution) >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5000 >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set nsample = 5000 >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> # Frequency with which MCMC path samples are >>>>>>>>>>>>>>>>>>>>>>>>>>> retained >>>>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5 (keep every 5th sample) >>>>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>>>> set nkeep = 5 >>>>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> The information in this e-mail is intended only for >>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>> person >>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>> whom >>>>>>>>>>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>> e-mail >>>>>>>>>>>>>>>>>>>>>>>>>> contains patient information, please contact the >>>>>>>>>>>>>>>>>>>>>>>>>> Partners >>>>>>>>>>>>>>>>>>>>>>>>>> Compliance >>>>>>>>>>>>>>>>>>>>>>>>>> HelpLine at >>>>>>>>>>>>>>>>>>>>>>>>>> http://www.partners.org/complianceline . If the >>>>>>>>>>>>>>>>>>>>>>>>>> e-mail >>>>>>>>>>>>>>>>>>>>>>>>>> was >>>>>>>>>>>>>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>>>>>>>>>>> but does not contain patient information, please >>>>>>>>>>>>>>>>>>>>>>>>>> contact >>>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>>> sender >>>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>>> properly >>>>>>>>>>>>>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> > > >

1 0

freesurfer atlases/versions
by Narly Golestani 28 Dec '12

28 Dec '12

Dear all, I have a quick question re- the different atlases used by the different versions of freesurfer. I'd like to know if there will be any differences in the auditory cortex labelization process if we use freesurfer version 4.5 and upwards. From the below post I have the impression that version 4.5 and upwards (until 5.2?) all apply similar rules for parcellating the 3 auditory cortex ROIs that we're interested in (the transverse temporal gyrus and sulcus, and the planum temporale). http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20932.html Thanks in advance for your input, with best wishes, Narly Golestani.

2 1

Re: [Freesurfer] clarifications about running bedpost instead of tracl-all step 2
by Anastasia Yendiki 28 Dec '12

28 Dec '12

Hi Prerona - I'm attaching a screenshot of your eigenvectors (dmri/dtifit_V1.nii.gz) on your FA map (dmri/dtifit_FA.nii.gz). I've marked the corpus callosum, where the eigenvectors should be oriented left to right, and the cingulum, where the eigenvectors should be oriented anterior to posterior. There's something wrong with your inputs, most likely the bvecs/bvals aren't correct. Hope this helps, a.y On Thu, 27 Dec 2012, s0675204 wrote: > Hi Anastasia, > > Thank you so much for your quick and excellent help, as usual. > > I am sorry to bother you again, but I looked at your emails on the > archives about this and they say that I should look at the gradient > tables and the eigenectors (dmri/dtifit_V1.nii.gz) > I looked at these but I could not spot a problem. Do you think it > would be possible for you to have a look if I uploaded my files? > > best wishes, > > Prerona > > > On 22 December 2012 11:04, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >> There are several threads about this in the archives. You need to look at >> the eigenectors in dmri/dtifit_V1.nii.gz and check that they are oriented in >> a way that makes sense with the anatomy. >> >> >> On Sat, 22 Dec 2012, s0675204 wrote: >> >>> Hi >>> >>> No I did not. Actually, I'm not sure how to do that. Is there any >>> information on that somewhere I could look up? >>> >>> best wishes, >>> >>> Prerona >>> >>> >>> On 21 December 2012 15:47, Anastasia Yendiki >>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> >>>> This doesn't look right. Are you certain that your gradient table is >>>> correct? Have you looked at the eigenvectors of the tensor fit to make >>>> sure >>>> they're in the right orientation? >>>> >>>> >>>> On Fri, 21 Dec 2012, s0675204 wrote: >>>> >>>>> Thank you so much for your help! Sorry if I asked something that has >>>>> already asked on the mailing list >>>>> >>>>> I tried changing the threshold but that did not help. I am following >>>>> exactly the instructions here >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs >>>>> >>>>> (Except I changed the file names >>>>> >>>>> So, the command I used was: >>>>> >>>>> freeview -v >>>>> /home/canlilab/SBU/data/tracula_test/00075/dmri/dtifit_FA.nii.gz \ >>>>> >>>>> >>>>> /home/canlilab/SBU/data/tracula_test/00075/dpath/lh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>> \ >>>>> >>>>> >>>>> /home/canlilab/SBU/data/tracula_test/00075/dpath/rh.ilf_AS_avg33_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>> &) >>>>> >>>>> Here is a screenshot attached. Should I also email you my files? >>>>> >>>>> best wishes, >>>>> >>>>> Prerona >>>>> >>>>> >>>>> On 20 December 2012 16:44, Anastasia Yendiki >>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> >>>>>> >>>>>> Hi Prerona - As I've mentioned to others, you can ignore the >>>>>> "Degenerate >>>>>> spline segment" message. >>>>>> >>>>>> I can't tell what you mean by "only traced a part of the trac". Can you >>>>>> see >>>>>> the rest of it when you play with the threshold? Are you reconstructing >>>>>> only >>>>>> the ILF? If not, do the other pathways look ok? Can you send a >>>>>> screenshot >>>>>> of >>>>>> what you see when you run the "freeview -tv ..." command from the >>>>>> tutorial? >>>>>> >>>>>> Thanks, >>>>>> a.y >>>>>> >>>>>> >>>>>> On Mon, 17 Dec 2012, s0675204 wrote: >>>>>> >>>>>>> Hello >>>>>>> >>>>>>> I have been running trac-paths, and thought it finishes with a message >>>>>>> saying no errors, >>>>>>> I get an error saying ERROR: Degenerate spline segment in the >>>>>>> intermediate message logs >>>>>>> >>>>>>> Also I looked at the result using this command: >>>>>>> freeview -v >>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \ >>>>>>> >>>>>>> >>>>>>> >>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>> \ >>>>>>> >>>>>>> >>>>>>> >>>>>>> $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' >>>>>>> & >>>>>>> >>>>>>> but it had only traced a part of the trac on one side and nothing on >>>>>>> the other side >>>>>>> >>>>>>> Can you help me understand what went wrong and how to fix it? >>>>>>> >>>>>>> Thank you so much for your help! >>>>>>> >>>>>>> best wishes, >>>>>>> >>>>>>> Prerona >>>>>>> >>>>>>> >>>>>>>>> On 12 December 2012 11:57, Anastasia Yendiki >>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 1) Can't hurt to delete. >>>>>>>>>> 2) Yes. >>>>>>>>>> 3) Yes. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Wed, 12 Dec 2012, s0675204 wrote: >>>>>>>>>> >>>>>>>>>>> Hello, >>>>>>>>>>> >>>>>>>>>>> thank you for your help with the first steps of running Tracula. >>>>>>>>>>> >>>>>>>>>>> I was trying to run trac-all step 3 (paths), but was getting an >>>>>>>>>>> error >>>>>>>>>>> with the mergedph1samples file. I saw on the mailbase that you >>>>>>>>>>> have >>>>>>>>>>> suggested to run bedpost directly to fix this >>>>>>>>>>> >>>>>>>>>>> I have 3 questions about this: >>>>>>>>>>> >>>>>>>>>>> 1) do I need to delete any of the (temporary?) files or folders >>>>>>>>>>> created by trac-all step 2 before running bedpost >>>>>>>>>>> >>>>>>>>>>> 2) should I run bedpost INSTEAD of trac-all step 2 for the >>>>>>>>>>> remaining >>>>>>>>>>> subjects? >>>>>>>>>>> >>>>>>>>>>> 3) you have suggested on the list to run bedpost as: >>>>>>>>>>> bedpostx /usr/local/freesurfer/subjects/C001/dmri >>>>>>>>>>> is this the same dmri folder as created by tracula step 1 (for >>>>>>>>>>> each >>>>>>>>>>> subject) >>>>>>>>>>> >>>>>>>>>>> Thank you so much for your help with this - I really appreciate it >>>>>>>>>>> >>>>>>>>>>> best wishes >>>>>>>>>>> >>>>>>>>>>> Prerona >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 10 December 2012 19:54, Anastasia Yendiki >>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> I'm guessing that this shows up in the scripts/trac-all.log of a >>>>>>>>>>>> particular >>>>>>>>>>>> subject? Then it applies to that subject. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Mon, 10 Dec 2012, s0675204 wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hello >>>>>>>>>>>>> >>>>>>>>>>>>> My trac- preproc has completed. However, I am confused about the >>>>>>>>>>>>> status message. It says: >>>>>>>>>>>>> >>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>> trac-preproc finished without error at Mon Dec 10 16:32:20 EST >>>>>>>>>>>>> 2012 >>>>>>>>>>>>> ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387 >>>>>>>>>>>>> >>>>>>>>>>>>> Does this mean it was completed succesfully for everyone or >>>>>>>>>>>>> everyone >>>>>>>>>>>>> but that 00387 person? >>>>>>>>>>>>> >>>>>>>>>>>>> Is there any way I can verify this? >>>>>>>>>>>>> >>>>>>>>>>>>> thank you so much for your help >>>>>>>>>>>>> >>>>>>>>>>>>> best wishes, >>>>>>>>>>>>> >>>>>>>>>>>>> Prerona >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 8 December 2012 13:38, Anastasia Yendiki >>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> In your dmrirc, you define multiple subjects, but only one >>>>>>>>>>>>>> bvecfile >>>>>>>>>>>>>> and >>>>>>>>>>>>>> one >>>>>>>>>>>>>> bvalfile that are used for all subjects. >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Sat, 8 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> the values are the same but each subject has an individual >>>>>>>>>>>>>>> bvec >>>>>>>>>>>>>>> & >>>>>>>>>>>>>>> bval >>>>>>>>>>>>>>> file. so it depends on how the script will read it? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 8 December 2012 00:03, Anastasia Yendiki >>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Are the bvecs/bvals not the same for all subjects? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> oh! i thought this was how these were meant to be! i will do >>>>>>>>>>>>>>>>> that. >>>>>>>>>>>>>>>>> sadly i left the lab and came home for the day but i will >>>>>>>>>>>>>>>>> try >>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>> as >>>>>>>>>>>>>>>>> soon as i am back and let you know! >>>>>>>>>>>>>>>>> thank you so much! do we have to do this for each subject or >>>>>>>>>>>>>>>>> just >>>>>>>>>>>>>>>>> one >>>>>>>>>>>>>>>>> time? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On 7 December 2012 23:51, Anastasia Yendiki >>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I see. Can you try formatting them in columns (1 column for >>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>> bvals >>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>> 3 >>>>>>>>>>>>>>>>>> columns for the bvecs)? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> yes! these are the original files >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> well these are the files i pointed to in my config file. >>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>> i >>>>>>>>>>>>>>>>>>> think >>>>>>>>>>>>>>>>>>> the script copies them over to the dmrirc folder? >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On 7 December 2012 23:38, Anastasia Yendiki >>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Yes, I can see that each of the bvecs/bvals files is one >>>>>>>>>>>>>>>>>>>> long >>>>>>>>>>>>>>>>>>>> line. >>>>>>>>>>>>>>>>>>>> Was >>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>> the case for the original files that you specified in the >>>>>>>>>>>>>>>>>>>> dmrirc? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hi Anastasia >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I had attached the files, but maybe they did not go >>>>>>>>>>>>>>>>>>>>> through >>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>> mailing list? So I am sending them to your email id. >>>>>>>>>>>>>>>>>>>>> Hope >>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>> okay >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>>>>>>>>>>>>> From: s0675204 <s0675204(a)sms.ed.ac.uk> >>>>>>>>>>>>>>>>>>>>> Date: 7 December 2012 19:44 >>>>>>>>>>>>>>>>>>>>> Subject: Re: [Freesurfer] Running Tracula: trac-preproc >>>>>>>>>>>>>>>>>>>>> exited >>>>>>>>>>>>>>>>>>>>> with >>>>>>>>>>>>>>>>>>>>> ERRORS >>>>>>>>>>>>>>>>>>>>> To: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Hello >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I think I spoke to soon! >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> It ended with errors again. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I get the error message: "bvecs and bvals don't have the >>>>>>>>>>>>>>>>>>>>> same >>>>>>>>>>>>>>>>>>>>> number >>>>>>>>>>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>>>>> entries" >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I saw on some older messages on the mail-base you said >>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>> we >>>>>>>>>>>>>>>>>>>>> need >>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>> check that the number of entries in the bvals is same as >>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>> bvecs >>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>> 3 times as much as the number of volumes. I have checked >>>>>>>>>>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>> the case >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I am wondering if it is some formatting problem? there >>>>>>>>>>>>>>>>>>>>> are >>>>>>>>>>>>>>>>>>>>> no >>>>>>>>>>>>>>>>>>>>> spaces >>>>>>>>>>>>>>>>>>>>> at the end of the file. and there are no end of line >>>>>>>>>>>>>>>>>>>>> markers >>>>>>>>>>>>>>>>>>>>> either. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Please could you advise me? I have attached the files >>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>> also >>>>>>>>>>>>>>>>>>>>> pasted >>>>>>>>>>>>>>>>>>>>> the contents below >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> My config file is still the same (as pasted below) >>>>>>>>>>>>>>>>>>>>> except >>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>> tried >>>>>>>>>>>>>>>>>>>>> changing >>>>>>>>>>>>>>>>>>>>> nb0 to 2 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> (# Number of low-b images >>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>> set nb0 = 2) >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> ========================================================= >>>>>>>>>>>>>>>>>>>>> bvals: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 0 800 800 800 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 800 800 0 800 800 800 800 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 >>>>>>>>>>>>>>>>>>>>> 800 800 800 800 800 800 >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> bvecs: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 0 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>>>>>>>>>>>>> 0.85177010297775 >>>>>>>>>>>>>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 >>>>>>>>>>>>>>>>>>>>> 0.7912425994873 >>>>>>>>>>>>>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>>>>>>>>>>>>> 0.44143822789192 >>>>>>>>>>>>>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 >>>>>>>>>>>>>>>>>>>>> 0.43744987249374 >>>>>>>>>>>>>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>>>>>>>>>>>>> 0.00979638285934 >>>>>>>>>>>>>>>>>>>>> 0 >>>>>>>>>>>>>>>>>>>>> 0.99864840507507 0.01463935524225 0.01274211052805 >>>>>>>>>>>>>>>>>>>>> 0.85177010297775 >>>>>>>>>>>>>>>>>>>>> 0.86449736356735 0.85295587778091 0.83894062042236 >>>>>>>>>>>>>>>>>>>>> 0.7912425994873 >>>>>>>>>>>>>>>>>>>>> 0.51641523838043 0.46147873997688 0.54209464788436 >>>>>>>>>>>>>>>>>>>>> 0.44143822789192 >>>>>>>>>>>>>>>>>>>>> 0.52723878622055 0.4250853061676 0.51590526103973 >>>>>>>>>>>>>>>>>>>>> 0.43744987249374 >>>>>>>>>>>>>>>>>>>>> 0.50455766916275 0.05208261311054 0.06073396280407 >>>>>>>>>>>>>>>>>>>>> 0.00979638285934 >>>>>>>>>>>>>>>>>>>>> 0 >>>>>>>>>>>>>>>>>>>>> -0.00687454920262 0.96709138154983 0.62002921104431 >>>>>>>>>>>>>>>>>>>>> 0.52092331647872 >>>>>>>>>>>>>>>>>>>>> 0.18501849472522 -0.42448142170906 -0.44344407320022 >>>>>>>>>>>>>>>>>>>>> 0.15539556741714 >>>>>>>>>>>>>>>>>>>>> 0.60610836744308 0.88347893953323 0.71210372447967 >>>>>>>>>>>>>>>>>>>>> 0.30400663614273 >>>>>>>>>>>>>>>>>>>>> -0.23736105859279 -0.70398008823394 -0.85636389255523 >>>>>>>>>>>>>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>>>>>>>>>>>>> 0.51328992843627 >>>>>>>>>>>>>>>>>>>>> 0.93218487501144 0 -0.00687454920262 0.96709138154983 >>>>>>>>>>>>>>>>>>>>> 0.62002921104431 >>>>>>>>>>>>>>>>>>>>> 0.52092331647872 0.18501849472522 -0.42448142170906 >>>>>>>>>>>>>>>>>>>>> -0.44344407320022 >>>>>>>>>>>>>>>>>>>>> 0.15539556741714 0.60610836744308 0.88347893953323 >>>>>>>>>>>>>>>>>>>>> 0.71210372447967 >>>>>>>>>>>>>>>>>>>>> 0.30400663614273 -0.23736105859279 -0.70398008823394 >>>>>>>>>>>>>>>>>>>>> -0.85636389255523 >>>>>>>>>>>>>>>>>>>>> -0.73376137018203 -0.22848516702652 -0.00803200621157 >>>>>>>>>>>>>>>>>>>>> 0.51328992843627 >>>>>>>>>>>>>>>>>>>>> 0.93218487501144 0 0.05151799321174 -0.2540076971054 >>>>>>>>>>>>>>>>>>>>> -0.78447526693344 >>>>>>>>>>>>>>>>>>>>> 0.05591572076082 -0.46734625101089 -0.3037790954113 >>>>>>>>>>>>>>>>>>>>> 0.31549325585365 >>>>>>>>>>>>>>>>>>>>> 0.5914282798767 0.60493636131286 0.08063688874244 >>>>>>>>>>>>>>>>>>>>> -0.44614082574844 >>>>>>>>>>>>>>>>>>>>> -0.84422290325164 -0.81589156389236 -0.56895911693573 >>>>>>>>>>>>>>>>>>>>> -0.02196817658841 0.51983833312988 0.83259600400924 >>>>>>>>>>>>>>>>>>>>> 0.99861049652099 >>>>>>>>>>>>>>>>>>>>> 0.85606354475021 0.36184993386268 0 0.05151799321174 >>>>>>>>>>>>>>>>>>>>> -0.2540076971054 >>>>>>>>>>>>>>>>>>>>> -0.78447526693344 0.05591572076082 -0.46734625101089 >>>>>>>>>>>>>>>>>>>>> -0.3037790954113 >>>>>>>>>>>>>>>>>>>>> 0.31549325585365 0.5914282798767 0.60493636131286 >>>>>>>>>>>>>>>>>>>>> 0.08063688874244 >>>>>>>>>>>>>>>>>>>>> -0.44614082574844 -0.84422290325164 -0.81589156389236 >>>>>>>>>>>>>>>>>>>>> -0.56895911693573 -0.02196817658841 0.51983833312988 >>>>>>>>>>>>>>>>>>>>> 0.83259600400924 >>>>>>>>>>>>>>>>>>>>> 0.99861049652099 0.85606354475021 0.36184993386268 >>>>>>>>>>>>>>>>>>>>> On 7 December 2012 14:08, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Great, I love easy problems :) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Thank you! It's chugging away now >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On 7 December 2012 13:46, Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>> <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hi Prerona - You need to uncomment the bvecfile and >>>>>>>>>>>>>>>>>>>>>>>> bvalfile >>>>>>>>>>>>>>>>>>>>>>>> definitions >>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>> your configuration file. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Hope this helps, >>>>>>>>>>>>>>>>>>>>>>>> a.y >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Fri, 7 Dec 2012, s0675204 wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Hello >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> I am trying to run Tracula on a set of dicoms files. >>>>>>>>>>>>>>>>>>>>>>>>> I >>>>>>>>>>>>>>>>>>>>>>>>> have >>>>>>>>>>>>>>>>>>>>>>>>> run >>>>>>>>>>>>>>>>>>>>>>>>> recon-all previously. >>>>>>>>>>>>>>>>>>>>>>>>> I am getting a message trac-preproc exited with >>>>>>>>>>>>>>>>>>>>>>>>> ERRORS >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Please can anyone advise me on this? >>>>>>>>>>>>>>>>>>>>>>>>> I have listed all the details (command, >>>>>>>>>>>>>>>>>>>>>>>>> error/output, >>>>>>>>>>>>>>>>>>>>>>>>> config >>>>>>>>>>>>>>>>>>>>>>>>> file) >>>>>>>>>>>>>>>>>>>>>>>>> below >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you so much for your help >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> best wishes, >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Prerona >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> DETAILS >>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>> command used: trac-all -prep -c >>>>>>>>>>>>>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>> error message >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> ========================================= >>>>>>>>>>>>>>>>>>>>>>>>> canlilab@112-205:~/SBU/data/tracula$ trac-all -prep >>>>>>>>>>>>>>>>>>>>>>>>> -c >>>>>>>>>>>>>>>>>>>>>>>>> ./scripts/dmrirc_single_subject >>>>>>>>>>>>>>>>>>>>>>>>> INFO: SUBJECTS_DIR is >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/recon_output >>>>>>>>>>>>>>>>>>>>>>>>> INFO: Diffusion root is >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula >>>>>>>>>>>>>>>>>>>>>>>>> Actual FREESURFER_HOME /home/canlilab/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>> trac-preproc -c >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/dmrirc.local >>>>>>>>>>>>>>>>>>>>>>>>> -log >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.log >>>>>>>>>>>>>>>>>>>>>>>>> -cmd >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/scripts/trac-all.cmd >>>>>>>>>>>>>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/freesurfer/bin/trac-preproc >>>>>>>>>>>>>>>>>>>>>>>>> #------------------------------------- >>>>>>>>>>>>>>>>>>>>>>>>> #@# Image corrections Fri Dec 7 10:42:30 EST 2012 >>>>>>>>>>>>>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> mri_convert >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 >>>>>>>>>>>>>>>>>>>>>>>>> greve >>>>>>>>>>>>>>>>>>>>>>>>> Exp >>>>>>>>>>>>>>>>>>>>>>>>> $ >>>>>>>>>>>>>>>>>>>>>>>>> reading from >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm... >>>>>>>>>>>>>>>>>>>>>>>>> Getting Series No >>>>>>>>>>>>>>>>>>>>>>>>> INFO: Found 44 files in >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075 >>>>>>>>>>>>>>>>>>>>>>>>> INFO: Scanning for Series Number 7 >>>>>>>>>>>>>>>>>>>>>>>>> Scanning Directory >>>>>>>>>>>>>>>>>>>>>>>>> INFO: found 42 files in series >>>>>>>>>>>>>>>>>>>>>>>>> INFO: loading series header info. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> RunNo = 6 >>>>>>>>>>>>>>>>>>>>>>>>> WARNING: Run 1 appears to be truncated >>>>>>>>>>>>>>>>>>>>>>>>> Files Found: 42, Files Expected (lRep+1): 2 >>>>>>>>>>>>>>>>>>>>>>>>> FileName >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> Identification >>>>>>>>>>>>>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>> Image information >>>>>>>>>>>>>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>>>>>>>>>>>>> ImgPos 772.3238 773.0634 185.5347 >>>>>>>>>>>>>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>>>>>>>>>>>>> VolCenter 0.0000 0.0000 0.0000 >>>>>>>>>>>>>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>>>>>>>>>>>>> INFO: sorting. >>>>>>>>>>>>>>>>>>>>>>>>> INFO: (128 128 40), nframes = 42, ismosaic=1 >>>>>>>>>>>>>>>>>>>>>>>>> Could not parse NUMARIS version string syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>> found in dicom tag 18,1020 (len = 3 != 6) >>>>>>>>>>>>>>>>>>>>>>>>> Repetition Time = 5500, TR = 5500 ms >>>>>>>>>>>>>>>>>>>>>>>>> PE Dir COL COL >>>>>>>>>>>>>>>>>>>>>>>>> AutoAlign matrix detected >>>>>>>>>>>>>>>>>>>>>>>>> AutoAlign Matrix --------------------- >>>>>>>>>>>>>>>>>>>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>>>>>>>>>>>>>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> FileName >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> Identification >>>>>>>>>>>>>>>>>>>>>>>>> NumarisVer syngo MR B17 >>>>>>>>>>>>>>>>>>>>>>>>> ScannerModel TrioTim >>>>>>>>>>>>>>>>>>>>>>>>> PatientName S790_P72_TC >>>>>>>>>>>>>>>>>>>>>>>>> Date and time >>>>>>>>>>>>>>>>>>>>>>>>> StudyDate 20120502 >>>>>>>>>>>>>>>>>>>>>>>>> StudyTime 120741.390000 >>>>>>>>>>>>>>>>>>>>>>>>> SeriesTime 125649.953000 >>>>>>>>>>>>>>>>>>>>>>>>> AcqTime 125626.150000 >>>>>>>>>>>>>>>>>>>>>>>>> Acquisition parameters >>>>>>>>>>>>>>>>>>>>>>>>> PulseSeq ep_b0 >>>>>>>>>>>>>>>>>>>>>>>>> Protocol DTI >>>>>>>>>>>>>>>>>>>>>>>>> PhEncDir COL >>>>>>>>>>>>>>>>>>>>>>>>> EchoNo 1 >>>>>>>>>>>>>>>>>>>>>>>>> FlipAngle 90 >>>>>>>>>>>>>>>>>>>>>>>>> EchoTime 93 >>>>>>>>>>>>>>>>>>>>>>>>> InversionTime -1 >>>>>>>>>>>>>>>>>>>>>>>>> RepetitionTime 5500 >>>>>>>>>>>>>>>>>>>>>>>>> PhEncFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>> ReadoutFOV 220 >>>>>>>>>>>>>>>>>>>>>>>>> Image information >>>>>>>>>>>>>>>>>>>>>>>>> RunNo 6 >>>>>>>>>>>>>>>>>>>>>>>>> SeriesNo 7 >>>>>>>>>>>>>>>>>>>>>>>>> ImageNo 1 >>>>>>>>>>>>>>>>>>>>>>>>> NImageRows 896 >>>>>>>>>>>>>>>>>>>>>>>>> NImageCols 896 >>>>>>>>>>>>>>>>>>>>>>>>> NFrames 42 >>>>>>>>>>>>>>>>>>>>>>>>> SliceArraylSize 40 >>>>>>>>>>>>>>>>>>>>>>>>> IsMosaic 1 >>>>>>>>>>>>>>>>>>>>>>>>> ImgPos 113.4156 146.2544 -24.5854 >>>>>>>>>>>>>>>>>>>>>>>>> VolRes 1.7188 1.7188 3.0000 >>>>>>>>>>>>>>>>>>>>>>>>> VolDim 128 128 40 >>>>>>>>>>>>>>>>>>>>>>>>> Vc -0.9983 0.0151 -0.0555 >>>>>>>>>>>>>>>>>>>>>>>>> Vr -0.0000 -0.9648 -0.2629 >>>>>>>>>>>>>>>>>>>>>>>>> Vs -0.0575 -0.2625 0.9632 >>>>>>>>>>>>>>>>>>>>>>>>> VolCenter 0.1478 26.0388 -1.8116 >>>>>>>>>>>>>>>>>>>>>>>>> TransferSyntaxUID 1.2.840.10008.1.2.1 >>>>>>>>>>>>>>>>>>>>>>>>> sagrev = 0, correv =0, trarev = 0 >>>>>>>>>>>>>>>>>>>>>>>>> Vs = -0.0574949 -0.262456 0.963229 >>>>>>>>>>>>>>>>>>>>>>>>> INFO: no Siemens slice order reversal detected >>>>>>>>>>>>>>>>>>>>>>>>> (good!). >>>>>>>>>>>>>>>>>>>>>>>>> TR=5500.00, TE=93.00, TI=-1.00, flip angle=90.00 >>>>>>>>>>>>>>>>>>>>>>>>> i_ras = (-0.998346, 0.0151149, -0.0554726) >>>>>>>>>>>>>>>>>>>>>>>>> j_ras = (-3.31902e-08, -0.964826, -0.262891) >>>>>>>>>>>>>>>>>>>>>>>>> k_ras = (-0.0574949, -0.262456, 0.963229) >>>>>>>>>>>>>>>>>>>>>>>>> writing to >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz... >>>>>>>>>>>>>>>>>>>>>>>>> mri_probedicom --i >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dcminfo.dat >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> flip4fsl >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> INFO: input image orientation is LPS >>>>>>>>>>>>>>>>>>>>>>>>> INFO: input image determinant is 8.86231 >>>>>>>>>>>>>>>>>>>>>>>>> fslswapdim >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> x -y z >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> INFO: left-right orientation was flipped by >>>>>>>>>>>>>>>>>>>>>>>>> fslswapdim >>>>>>>>>>>>>>>>>>>>>>>>> fslorient -forceradiological >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> mv -f >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>>>>>>>>>>>>>>>>>>> /home/canlilab/SBU/data/tracula/00075/dmri/bvecs >>>>>>>>>>>>>>>>>>>>>>>>> mv: cannot stat >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> `/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs': >>>>>>>>>>>>>>>>>>>>>>>>> No such file or directory >>>>>>>>>>>>>>>>>>>>>>>>> Linux 112-205.psy.sunysb.edu >>>>>>>>>>>>>>>>>>>>>>>>> 2.6.32-279.5.2.el6.x86_64 >>>>>>>>>>>>>>>>>>>>>>>>> #1 >>>>>>>>>>>>>>>>>>>>>>>>> SMP >>>>>>>>>>>>>>>>>>>>>>>>> Fri >>>>>>>>>>>>>>>>>>>>>>>>> Aug >>>>>>>>>>>>>>>>>>>>>>>>> 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> trac-preproc exited with ERRORS at Fri Dec 7 >>>>>>>>>>>>>>>>>>>>>>>>> 10:42:51 >>>>>>>>>>>>>>>>>>>>>>>>> EST >>>>>>>>>>>>>>>>>>>>>>>>> 2012 >>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> config file: >>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # dmrirc.example >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # This file contains commands that will be run by >>>>>>>>>>>>>>>>>>>>>>>>> trac-all >>>>>>>>>>>>>>>>>>>>>>>>> before >>>>>>>>>>>>>>>>>>>>>>>>> an >>>>>>>>>>>>>>>>>>>>>>>>> analysis. >>>>>>>>>>>>>>>>>>>>>>>>> # It is used to set all parameters needed for the >>>>>>>>>>>>>>>>>>>>>>>>> analysis. >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Remove a parameter from your dmrirc file if you >>>>>>>>>>>>>>>>>>>>>>>>> want >>>>>>>>>>>>>>>>>>>>>>>>> use >>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>> default >>>>>>>>>>>>>>>>>>>>>>>>> value. >>>>>>>>>>>>>>>>>>>>>>>>> # Parameters that don't have default values must be >>>>>>>>>>>>>>>>>>>>>>>>> specified. >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Any other commands that you might want to run >>>>>>>>>>>>>>>>>>>>>>>>> before >>>>>>>>>>>>>>>>>>>>>>>>> an >>>>>>>>>>>>>>>>>>>>>>>>> analysis >>>>>>>>>>>>>>>>>>>>>>>>> can >>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>> added >>>>>>>>>>>>>>>>>>>>>>>>> # to this file. >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Original Author: Anastasia Yendiki >>>>>>>>>>>>>>>>>>>>>>>>> # CVS Revision Info: >>>>>>>>>>>>>>>>>>>>>>>>> # $Author: ayendiki $ >>>>>>>>>>>>>>>>>>>>>>>>> # $Date: 2011/05/24 06:47:12 $ >>>>>>>>>>>>>>>>>>>>>>>>> # $Revision: 1.3.2.3 $ >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Copyright © 2011 The General Hospital Corporation >>>>>>>>>>>>>>>>>>>>>>>>> (Boston >>>>>>>>>>>>>>>>>>>>>>>>> MA) >>>>>>>>>>>>>>>>>>>>>>>>> "MGH" >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Terms and conditions for use reproduction >>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>> contribution >>>>>>>>>>>>>>>>>>>>>>>>> # are found in the 'FreeSurfer Software License >>>>>>>>>>>>>>>>>>>>>>>>> Agreement' >>>>>>>>>>>>>>>>>>>>>>>>> contained >>>>>>>>>>>>>>>>>>>>>>>>> # in the file 'LICENSE' found in the FreeSurfer >>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>> here: >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # Reporting: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # FreeSurfer SUBJECTS_DIR >>>>>>>>>>>>>>>>>>>>>>>>> # T1 images and FreeSurfer segmentations are >>>>>>>>>>>>>>>>>>>>>>>>> expected >>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>> be >>>>>>>>>>>>>>>>>>>>>>>>> found >>>>>>>>>>>>>>>>>>>>>>>>> here >>>>>>>>>>>>>>>>>>>>>>>>> # setenv SUBJECTS_DIR /path/to/recons/of/ducks >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Output directory where trac-all results will be >>>>>>>>>>>>>>>>>>>>>>>>> saved >>>>>>>>>>>>>>>>>>>>>>>>> # Default: Same as SUBJECTS_DIR >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set dtroot = $pre_data/tracula >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Subject IDs >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set subjlist = (00075 00104 00122 00200 00308 00369 >>>>>>>>>>>>>>>>>>>>>>>>> 00387 >>>>>>>>>>>>>>>>>>>>>>>>> 00400 >>>>>>>>>>>>>>>>>>>>>>>>> 00422 >>>>>>>>>>>>>>>>>>>>>>>>> 00452 00518 00568 00587 00624 00636 00686 00698 >>>>>>>>>>>>>>>>>>>>>>>>> 00727 >>>>>>>>>>>>>>>>>>>>>>>>> 00909 >>>>>>>>>>>>>>>>>>>>>>>>> 00926 >>>>>>>>>>>>>>>>>>>>>>>>> 00933 00943 00983 00992 01049 01121 01329 01450 >>>>>>>>>>>>>>>>>>>>>>>>> 01509 >>>>>>>>>>>>>>>>>>>>>>>>> 01531 >>>>>>>>>>>>>>>>>>>>>>>>> 01678 >>>>>>>>>>>>>>>>>>>>>>>>> 01735 01746 01809 01843 01917 10039 10056 10089 >>>>>>>>>>>>>>>>>>>>>>>>> 10165 >>>>>>>>>>>>>>>>>>>>>>>>> 10171 >>>>>>>>>>>>>>>>>>>>>>>>> 10227 >>>>>>>>>>>>>>>>>>>>>>>>> 10238 10263 10314 10320 10326 10349 10407 10431 >>>>>>>>>>>>>>>>>>>>>>>>> 10435 >>>>>>>>>>>>>>>>>>>>>>>>> 10458 >>>>>>>>>>>>>>>>>>>>>>>>> 10477 >>>>>>>>>>>>>>>>>>>>>>>>> 10499 10500 10636 10750 11209 12210 12357 12472 >>>>>>>>>>>>>>>>>>>>>>>>> 12645 >>>>>>>>>>>>>>>>>>>>>>>>> 13493 >>>>>>>>>>>>>>>>>>>>>>>>> 13958 >>>>>>>>>>>>>>>>>>>>>>>>> 14302 14481 14530 15329 15345 15864 16654 17267 >>>>>>>>>>>>>>>>>>>>>>>>> 17478 >>>>>>>>>>>>>>>>>>>>>>>>> 18337 >>>>>>>>>>>>>>>>>>>>>>>>> 18422 >>>>>>>>>>>>>>>>>>>>>>>>> 18530 19259 19377 19725 20071 20383 21413 23846 >>>>>>>>>>>>>>>>>>>>>>>>> 24115 >>>>>>>>>>>>>>>>>>>>>>>>> 24531 >>>>>>>>>>>>>>>>>>>>>>>>> 24781 >>>>>>>>>>>>>>>>>>>>>>>>> 25962 26314 26475 28822 30510 30571 30927 31034 >>>>>>>>>>>>>>>>>>>>>>>>> 31049 >>>>>>>>>>>>>>>>>>>>>>>>> 31237 >>>>>>>>>>>>>>>>>>>>>>>>> 31437 >>>>>>>>>>>>>>>>>>>>>>>>> 31471 31531 32131 32162 32222) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # In case you want to analyze only Huey and Louie >>>>>>>>>>>>>>>>>>>>>>>>> # Default: Run analysis on all subjects >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set runlist = (1 2 3 4 5 >>>>>>>>>>>>>>>>>>>>>>>>> 6 >>>>>>>>>>>>>>>>>>>>>>>>> 7 >>>>>>>>>>>>>>>>>>>>>>>>> 8 9 10 11 12 13 14 >>>>>>>>>>>>>>>>>>>>>>>>> 15 >>>>>>>>>>>>>>>>>>>>>>>>> 16 >>>>>>>>>>>>>>>>>>>>>>>>> 17 18 19 20 21 22 23 >>>>>>>>>>>>>>>>>>>>>>>>> 24 >>>>>>>>>>>>>>>>>>>>>>>>> 25 >>>>>>>>>>>>>>>>>>>>>>>>> 26 27 28 29 30 31 32 >>>>>>>>>>>>>>>>>>>>>>>>> 33 >>>>>>>>>>>>>>>>>>>>>>>>> 34 >>>>>>>>>>>>>>>>>>>>>>>>> 35 36 37 38 39 40 41 >>>>>>>>>>>>>>>>>>>>>>>>> 42 >>>>>>>>>>>>>>>>>>>>>>>>> 43 >>>>>>>>>>>>>>>>>>>>>>>>> 44 45 46 47 48 49 >>>>>>>>>>>>>>>>>>>>>>>>> 50 >>>>>>>>>>>>>>>>>>>>>>>>> 51 >>>>>>>>>>>>>>>>>>>>>>>>> 52 >>>>>>>>>>>>>>>>>>>>>>>>> 53 54 55 56 57 58 >>>>>>>>>>>>>>>>>>>>>>>>> 59 >>>>>>>>>>>>>>>>>>>>>>>>> 60 >>>>>>>>>>>>>>>>>>>>>>>>> 61 62 63 64 65 66 67 >>>>>>>>>>>>>>>>>>>>>>>>> 68 >>>>>>>>>>>>>>>>>>>>>>>>> 69 >>>>>>>>>>>>>>>>>>>>>>>>> 70 71 72 73 74 75 76 >>>>>>>>>>>>>>>>>>>>>>>>> 77 >>>>>>>>>>>>>>>>>>>>>>>>> 78 >>>>>>>>>>>>>>>>>>>>>>>>> 79 80 81 82 83 84 85 >>>>>>>>>>>>>>>>>>>>>>>>> 86 >>>>>>>>>>>>>>>>>>>>>>>>> 87 >>>>>>>>>>>>>>>>>>>>>>>>> 88 89 90 91 92 93 94 >>>>>>>>>>>>>>>>>>>>>>>>> 95 >>>>>>>>>>>>>>>>>>>>>>>>> 96 >>>>>>>>>>>>>>>>>>>>>>>>> 97 98 99 100 101 102) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Input diffusion DICOMs (file names relative to >>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>> # If original DICOMs don't exist these can be in >>>>>>>>>>>>>>>>>>>>>>>>> other >>>>>>>>>>>>>>>>>>>>>>>>> image >>>>>>>>>>>>>>>>>>>>>>>>> format >>>>>>>>>>>>>>>>>>>>>>>>> # but then bvecfile bvalfile and nb0 must be >>>>>>>>>>>>>>>>>>>>>>>>> specified >>>>>>>>>>>>>>>>>>>>>>>>> (see >>>>>>>>>>>>>>>>>>>>>>>>> below) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> set dcmroot = $pre_data/dti_dicoms >>>>>>>>>>>>>>>>>>>>>>>>> set dcmlist = (00075/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00104/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00122/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00200/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00308/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00369/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00387/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00400/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00422/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00452/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00518/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00568/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00587/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00624/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00636/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00686/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00698/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00727/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00909/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00926/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00933/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00943/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00983/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 00992/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01049/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01121/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01329/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01450/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01509/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01678/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01735/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01746/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01809/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01843/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 01917/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10039/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10056/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10089/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10165/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10171/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10227/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10238/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10263/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10314/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10320/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10326/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10349/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10407/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10431/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10435/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10458/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10477/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10499/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10500/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10636/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 10750/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 11209/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 12210/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 12357/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 12472/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 12645/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 13493/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 13958/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 14302/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 14481/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 14530/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 15329/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 15345/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 15864/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 16654/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 17267/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 17478/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 18337/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 18422/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 18530/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 19259/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 19377/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 19725/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 20071/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 20383/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 21413/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 23846/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 24115/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 24531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 24781/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 25962/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 26314/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 26475/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 28822/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 30510/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 30571/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 30927/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31034/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31049/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31237/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31437/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31471/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 31531/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 32131/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 32162/data_1.dcm \ >>>>>>>>>>>>>>>>>>>>>>>>> 32222/data_1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Diffusion gradient table >>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not MGH DICOMs >>>>>>>>>>>>>>>>>>>>>>>>> # Three-column format one row for each volume in the >>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>> set >>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> #set bvecfile = >>>>>>>>>>>>>>>>>>>>>>>>> $pre_data/DTI_Analysis/00075/bvecs.txt >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Diffusion b-value table >>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not MGH DICOMs >>>>>>>>>>>>>>>>>>>>>>>>> # Single-column format one value for each volume in >>>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>> data >>>>>>>>>>>>>>>>>>>>>>>>> set >>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> #set bvalfile = >>>>>>>>>>>>>>>>>>>>>>>>> $pre_data/DTI_Analysis/00075/bvals.txt >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Number of low-b images >>>>>>>>>>>>>>>>>>>>>>>>> # Must be specified if inputs are not DICOM >>>>>>>>>>>>>>>>>>>>>>>>> # Default: Read from DICOM header >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set nb0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Perform registration-based B0-inhomogeneity >>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set dob0 = 0 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Input B0 field map magnitude DICOMs (file names >>>>>>>>>>>>>>>>>>>>>>>>> relative >>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> #set b0mlist = (huey/fmag/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> dewey/fmag/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> louie/fmag/XXX-1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Input B0 field map phase DICOMs (file names >>>>>>>>>>>>>>>>>>>>>>>>> relative >>>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>>> dcmroot) >>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> #set b0plist = (huey/fphas/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> dewey/fphas/XXX-1.dcm >>>>>>>>>>>>>>>>>>>>>>>>> louie/fphas/XXX-1.dcm) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Echo spacing for field mapping sequence (from >>>>>>>>>>>>>>>>>>>>>>>>> sequence >>>>>>>>>>>>>>>>>>>>>>>>> printout) >>>>>>>>>>>>>>>>>>>>>>>>> # Only used if dob0 = 1 >>>>>>>>>>>>>>>>>>>>>>>>> # Default: None >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> #set echospacing = 0.7 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Perform registration-based eddy-current >>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set doeddy = 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Rotate diffusion gradient vectors to match >>>>>>>>>>>>>>>>>>>>>>>>> eddy-current >>>>>>>>>>>>>>>>>>>>>>>>> compensation? >>>>>>>>>>>>>>>>>>>>>>>>> # Only used if doeddy = 1 >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set dorotbvecs = 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Fractional intensity threshold for BET mask >>>>>>>>>>>>>>>>>>>>>>>>> extraction >>>>>>>>>>>>>>>>>>>>>>>>> from >>>>>>>>>>>>>>>>>>>>>>>>> low-b >>>>>>>>>>>>>>>>>>>>>>>>> images >>>>>>>>>>>>>>>>>>>>>>>>> # This mask is used only if usemaskanat = 0 >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0.3 >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set thrbet = 0.5 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by flirt? >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set doregflt = 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Perform diffusion-to-T1 registration by >>>>>>>>>>>>>>>>>>>>>>>>> bbregister? >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set doregbbr = 0 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # MNI template (the only option for inter-subject >>>>>>>>>>>>>>>>>>>>>>>>> registration >>>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>>> this >>>>>>>>>>>>>>>>>>>>>>>>> version) >>>>>>>>>>>>>>>>>>>>>>>>> # Default: >>>>>>>>>>>>>>>>>>>>>>>>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set mnitemp = >>>>>>>>>>>>>>>>>>>>>>>>> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Use brain mask extracted from T1 image instead of >>>>>>>>>>>>>>>>>>>>>>>>> low-b >>>>>>>>>>>>>>>>>>>>>>>>> diffusion >>>>>>>>>>>>>>>>>>>>>>>>> image? >>>>>>>>>>>>>>>>>>>>>>>>> # Has no effect if there is no T1 data >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 1 (yes) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set usemaskanat = 1 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Paths to reconstruct >>>>>>>>>>>>>>>>>>>>>>>>> # Default: All paths in the atlas >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set pathlist = ( lh.cst_AS rh.cst_AS \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.unc_AS rh.unc_AS \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.ilf_AS rh.ilf_AS \ >>>>>>>>>>>>>>>>>>>>>>>>> fmajor_PP fminor_PP \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.atr_PP rh.atr_PP \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.ccg_PP rh.ccg_PP \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.cab_PP rh.cab_PP \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.slfp_PP rh.slfp_PP \ >>>>>>>>>>>>>>>>>>>>>>>>> lh.slft_PP rh.slft_PP ) >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Number of path control points >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5 >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set ncpts = 5 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # List of training subjects >>>>>>>>>>>>>>>>>>>>>>>>> # This text file lists the locations of training >>>>>>>>>>>>>>>>>>>>>>>>> subject >>>>>>>>>>>>>>>>>>>>>>>>> directories >>>>>>>>>>>>>>>>>>>>>>>>> # Default: $FREESURFER_HOME/trctrain/trainlist.txt >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set trainfile = >>>>>>>>>>>>>>>>>>>>>>>>> $FREESURFER_HOME/trctrain/trainlist.txt >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Use long (more descriptive) directory hierarchy >>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>> saving >>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>> distributions? >>>>>>>>>>>>>>>>>>>>>>>>> # By default paths distributions are saved directly >>>>>>>>>>>>>>>>>>>>>>>>> under >>>>>>>>>>>>>>>>>>>>>>>>> $subjectname/dpath >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 0 (no) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set dopathsubdirs = 0 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Number of MCMC burn-in iterations >>>>>>>>>>>>>>>>>>>>>>>>> # (Path samples drawn initially by MCMC algorithm >>>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>>> discarded) >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 200 >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set nburnin = 200 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Number of MCMC iterations >>>>>>>>>>>>>>>>>>>>>>>>> # (Path samples drawn by MCMC algorithm and used to >>>>>>>>>>>>>>>>>>>>>>>>> estimate >>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>> distribution) >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5000 >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set nsample = 5000 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> # Frequency with which MCMC path samples are >>>>>>>>>>>>>>>>>>>>>>>>> retained >>>>>>>>>>>>>>>>>>>>>>>>> for >>>>>>>>>>>>>>>>>>>>>>>>> path >>>>>>>>>>>>>>>>>>>>>>>>> distribution >>>>>>>>>>>>>>>>>>>>>>>>> # Default: 5 (keep every 5th sample) >>>>>>>>>>>>>>>>>>>>>>>>> # >>>>>>>>>>>>>>>>>>>>>>>>> set nkeep = 5 >>>>>>>>>>>>>>>>>>>>>>>>> ============================================== >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>>>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> The information in this e-mail is intended only for >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> person >>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>> whom >>>>>>>>>>>>>>>>>>>>>>>> it >>>>>>>>>>>>>>>>>>>>>>>> is >>>>>>>>>>>>>>>>>>>>>>>> addressed. If you believe this e-mail was sent to you >>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> e-mail >>>>>>>>>>>>>>>>>>>>>>>> contains patient information, please contact the >>>>>>>>>>>>>>>>>>>>>>>> Partners >>>>>>>>>>>>>>>>>>>>>>>> Compliance >>>>>>>>>>>>>>>>>>>>>>>> HelpLine at >>>>>>>>>>>>>>>>>>>>>>>> http://www.partners.org/complianceline . If the >>>>>>>>>>>>>>>>>>>>>>>> e-mail >>>>>>>>>>>>>>>>>>>>>>>> was >>>>>>>>>>>>>>>>>>>>>>>> sent >>>>>>>>>>>>>>>>>>>>>>>> to >>>>>>>>>>>>>>>>>>>>>>>> you >>>>>>>>>>>>>>>>>>>>>>>> in >>>>>>>>>>>>>>>>>>>>>>>> error >>>>>>>>>>>>>>>>>>>>>>>> but does not contain patient information, please >>>>>>>>>>>>>>>>>>>>>>>> contact >>>>>>>>>>>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>>>>>>>>>> sender >>>>>>>>>>>>>>>>>>>>>>>> and >>>>>>>>>>>>>>>>>>>>>>>> properly >>>>>>>>>>>>>>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >>> >>> >> > > >

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Freesurfer December 2012